X-ray Structure of Polypeptide Deformylase

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

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Discovery of piperazic acid peptide deformylase inhibitors with in vivo activity for respiratory tract and skin infections.

Spletstoser, J.T.Dreabit, J.Knox, A.N.Benowitz, A.Campobasso, N.Ward, P.Cui, G.Lewandowski, T.McCloskey, L.Aubart, K.M.

(2019) Bioorg Med Chem Lett 29: 2410-2414

  • DOI: https://doi.org/10.1016/j.bmcl.2019.05.028
  • Primary Citation of Related Structures:  
    6OW2, 6OW7

  • PubMed Abstract: 

    The discovery of a novel series of peptide deformylase inhibitors incorporating a piperazic acid amino acid found in nature is described. These compounds demonstrated potent in vitro enzymatic potency and antimicrobial activity. Crystal structure analysis revealed the piperazic acid optimized a key contact with the PDF protein that accounted for the increased enzymatic potency of these compounds. We describe lead optimization of the P3' region of the series that resulted in a compound with good potency against three target organisms. One molecule showed in vivo efficacy in a rat respiratory infection model but ultimately did not meet candidate progression criteria.

  • Organizational Affiliation

    GlaxoSmithKline, 1250 S. Collegeville Rd., Collegeville, PA 19426, USA. Electronic address: jared.t.spletstoser@gsk.com.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide deformylaseA [auth P]202Streptococcus pneumoniaeMutation(s): 0 
Gene Names: 
Find proteins for Q8DP79 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore Q8DP79 
Go to UniProtKB:  Q8DP79
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DP79
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NB4 (Subject of Investigation/LOI)
Query on NB4

Download Ideal Coordinates CCD File 
C [auth P](2R)-2-(cyclopentylmethyl)-N'-{5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methylpyrimidin-4-yl}-3-[hydroxy(hydroxymethyl)amino]propanehydrazide
C22 H36 F N7 O4
Query on NI

Download Ideal Coordinates CCD File 
Binding Affinity Annotations 
IDSourceBinding Affinity
NB4 Binding MOAD:  6OW2 IC50: 3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.334α = 90
b = 50.334β = 90
c = 91.482γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-08-21
    Changes: Data collection, Database references